Searching for signals of evolutionary selection in 168 genes related to immune function.

Pathogens have played a substantial role in human evolution, with past infections shaping genetic variation at loci influencing immune function. We selected 168 genes known to be involved in the immune response, genotyped common single nucleotide polymorphisms across each gene in three population samples (CEPH Europeans from Utah, Han Chinese from Guangxi, and Yoruba Nigerians from Southwest Nigeria) and searched for evidence of selection based on four tests for non-neutral evolution: minor allele frequency (MAF), derived allele frequency (DAF), Fst versus heterozygosity and extended haplotype homozygosity (EHH). Six of the 168 genes show some evidence for non-neutral evolution in this initial screen, with two showing similar signals in independent data from the International HapMap Project. These analyses identify two loci involved in immune function that are candidates for having been subject to evolutionary selection, and highlight a number of analytical challenges in searching for selection in genome-wide polymorphism data

Comparisons with Empirical and Simulation Data

<div><p>(A) and (B) Plots of relative EHH versus frequency for <i>CCR5</i> in comparison to HapMap data (release 16) for Chromosome 3 in European-Americans (A) and 1,000 simulations of 400 chromosomes in European-Americans (B). Green dots represent the comparison haplotypes and the lines represent, from bottom to top, the 50th, 75th, 95th, and 99th percentiles. The red dots represent the results for eight <i>CCR5-</i>Δ<i>32</i>-bearing chromosomes in (A) and 32 <i>CCR5-</i>Δ<i>32</i>-bearing chromosomes in (B) for the centromere-proximal side, and the blue dots represent results for the centromere-distal side.</p> <p>(C) EHL of the haplotypes of frequency 6%–10% from the HapMap (solid green line) and from simulations (dotted green line) in comparison to <i>CCR5-</i>Δ<i>32</i> (red line).</p></div

EHH Breakdown of EHH over Distance between the <i>CCR5-</i>Δ<i>32</i> Mutation and 63 SNPs at Increasing Distances from the Mutation

<div><p>(A) Map of SNPs typed.</p> <p>(B) Comparison between Δ<i>32</i> and a single non-Δ<i>32</i> class of haplotypes. It should be noted that the Δ<i>32</i>-bearing chromosomes appear (red) to have greatly extended LD compared to the non-Δ<i>32</i>-bearing chromosomes (black).</p> <p>(C) Breakdown using the eight-marker haplotype containing the Δ<i>32</i> mutation. There are five haplotypes in European-Americans (frequencies: 42%, 31%, 10%, 8%, and 8%, respectively). Full haplotype sequences and frequencies in other populations are given in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030378#st003" target="_blank">Table S3</a>. Notice that two of the non-Δ<i>32</i>-bearing chromosomes (black) appear to have the similar extended LD when compared to the Δ<i>32</i>-bearing chromosomes centromere-distal to <i>CCR5</i> (red). Centromere-proximal Δ<i>32</i>-bearing chromosomes still have the most extended LD, indicated with an arrow.</p></div

Model of Haplotype-Based Selection Approach

<p>The image compares this approach, where the variants at the gene being studied are fully elaborated, to a model where the variants are not fully elaborated. At the top, multiple SNPs are genotyped to fully define the variants that exist in the gene. The resultant observed haplotype structure is shown in both bifurcation diagram and EHH plot formats (see <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0030378#s3" target="_blank">Materials and Methods</a>). At the bottom, only one SNP is genotyped, collapsing all other variants into a seemingly diverse super-haplotype and creating an impression of extension for the remaining haplotype.</p

A Systematic Screen of FDA-Approved Drugs for Inhibitors of Biological Threat Agents

<div><p>Background</p><p>The rapid development of effective medical countermeasures against potential biological threat agents is vital. Repurposing existing drugs that may have unanticipated activities as potential countermeasures is one way to meet this important goal, since currently approved drugs already have well-established safety and pharmacokinetic profiles in patients, as well as manufacturing and distribution networks. Therefore, approved drugs could rapidly be made available for a new indication in an emergency.</p> <p>Methodology/Principal Findings</p><p>A large systematic effort to determine whether existing drugs can be used against high containment bacterial and viral pathogens is described. We assembled and screened 1012 FDA-approved drugs for off-label broad-spectrum efficacy against <i>Bacillus anthracis</i>; <i>Francisella tularensis</i>; <i>Coxiella burnetii</i>; and Ebola, Marburg, and Lassa fever viruses using <i>in vitro</i> cell culture assays. We found a variety of hits against two or more of these biological threat pathogens, which were validated in secondary assays. As expected, antibiotic compounds were highly active against bacterial agents, but we did not identify any non-antibiotic compounds with broad-spectrum antibacterial activity. Lomefloxacin and erythromycin were found to be the most potent compounds <i>in vivo</i> protecting mice against <i>Bacillus anthracis</i> challenge. While multiple virus-specific inhibitors were identified, the most noteworthy antiviral compound identified was chloroquine, which disrupted entry and replication of two or more viruses <i>in vitro</i> and protected mice against Ebola virus challenge <i>in vivo</i>.</p> <p>Conclusions/Significance</p><p>The feasibility of repurposing existing drugs to face novel threats is demonstrated and this represents the first effort to apply this approach to high containment bacteria and viruses.</p> </div

Broad-spectrum compounds active against two or more viruses.

a<p>NT: Not tested; –: No protection; +: protection; VPEN: viral pseudotype entry assay; VR: viral replication assay.</p

Schematic diagram of the drug-repurposing screen.

<p>Schematic diagram of the drug-repurposing screen.</p